I generally only ban spells when it's obvious that they're way too overpowered. A good example of this is scorching ray. My players loved it until half the party (at an APL of 6) was wiped out by a single 4th-level sorcerer with scorching ray. IMO, 4d6 damage on a ranged touch attack is just too good for a 2nd-level spell. Acid arrow and flaming sphere aren't nearly that good (athough flaming sphere might come close, it deals damage over several turns), which I consider to be the benchmark energy damage spells for 2nd level.
I don't ban polymorph spells, but I do require that PC's wanting to cast it have to have stat blocks on paper that they can hand me for their different forms. This policy generally restricts spellcasters with it to two or three forms, with the added benefit that the player actually learns the ins and outs of their different forms. Works for my games.
I banned teleport and greater teleport after a year or so of deliberation. It's not unbalanced, it's just too plot-busting. Higher-level campaigns usually devolve into figuring out the adventure goal, scrying the revelant sites, and teleporting from one to one in quick succession. Some players have criticized me for this as lazy design. But there's only so many adventures where the players have to spend a session or two figuring out the real goal, involving divination-blocked sites, or magical interference that prohibits teleporting. Travel and exploration is one of my favorite parts of D&D, and teleport just takes it out of the equation.
I've also generally banned raise dead, resurrection, and similar effects. This is mostly a flavor issue. I just got tired of seeing players sock back 5,000 gp in diamonds and from then on charge headlong into certain death. Grisly deaths in pools of acid, at the hands of undead and the like brought accusations that I was "deliberately" killing their characters in a fashion so they couldn't be raised from the dead. I've never seen a character in a fantasy movie or novel say, "Oh, I might be able to survive that sprint across that pool of acid. Just fish my body out if I don't and hit up the temple of Pelor." I don't expect my characters to act this way either. I still allow raise dead and the like, but they can only be cast under very specific circumstances: in sanctified places on holy days (of which there are only 3-4 a year for any given faith). Until then, you'd best hope your cleric don't mind casting gentle repose on you every few days.
I also generally try to avoid save-or-die effects. They're just not fun or satisfying for me or the players.